Genome-wide association analysis with a dense marker set, mapping by admixture linkage disequilibrium (MALD) with ancestry informative markers, and examination of candidate gene analysis each requires a high-throughput genotyping laboratory. Utilizing the core laboratory we have developed at the Laboratory of Genomic Diversity (LGD) has allowed determination and publication of a MALD map for disease gene discovery in African Americans. Our collaborators have now used that map and the MALD method for gene identification in prostate cancer and IL-6 levels along with gene localization in multiple sclerosis. Ongoing efforts in our laboratory are applying the MALD technology to HIV/AIDS, Hepatitis C virus (HCV), focal segmental glomerulosclerosis, and end-stage renal disease. The laboratory has also undertaken candidate gene analysis for HIV-1, HCV, HBV and cardiovascular disease complications of end-stage renal disease.